Abstract
Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.
Highlights
Domestic chickens are the most common poultry and are valuable sources of protein for humans
As relatively few cultivated specimens of chicken gastrointestinal tract (GIT) microbes are available mainly due to their requirement for anaerobic conditions similar to those in the GIT, researchers have turned to new culture-independent approaches, metagenomics, to predict nutritional and ecological roles of GIT microbes
Conventional, low-throughput Sanger sequencing method has been limited in metagenomic studies of GIT microbiota due to high sequencing costs and insufficient sequence data
Summary
Domestic chickens are the most common poultry and are valuable sources of protein for humans. Conventional, low-throughput Sanger sequencing method has been limited in metagenomic studies of GIT microbiota due to high sequencing costs and insufficient sequence data. Newly developed sequencing platforms such as next-generation sequencing (NGS) have allowed the substantial researches into the diversity and functions of microbiota from the guts of various livestock animals. High-throughput NGS generates large volumes sequence data containing genetic information (Metzker, 2010), and this allows hypothesis-driven researches on chicken GIT microbiota, thereby highlighting the roles of previously unknown and rare microbial GIT species (Sogin et al, 2006; Medinger et al, 2010). We review the current status on metagenomics-driven studies on chicken GIT’s microbiota and the involved methodology, and suggest possible approaches for better understanding of GIT microbiota to increase chicken productivity and overall health
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